A scanning probe microscope (SPM) is used to measure the detailed shape and properties of a sample surface. Examples of a scanning probe microscope includes a scanning tunneling microscope (STM) and an atomic force microscope (AFM). The STM measures physical phenomena, such as current (tunneling current), by arranging a sharp tip of a probe near a sample (specimen) and measuring the shape and properties of the sample surface at the atomic level. The AFM enables observation of an insulating sample, which is difficult to measure with the STM, with an accuracy equivalent to the size of an atom (refer to, for example, Patent Document 1). By using the scanning probe microscope, the state of molecules adsorbed on the surface of a known object can also be evaluated.
The resolution and stability of a scanning probe microscope is greatly affected by the tip of a probe. The tip of a probe is required to be sharp at the atomic level, and an atom at the probe tip is required to be stable. Many techniques have been developed to manufacture a desirable probe (refer to, for example, Patent Documents 2 and 3).
However, it is normally difficult to manufacture a sharp probe at the atomic level. Even if such a probe can be manufactured, a scanning probe microscope using such a probe may fail to form a measurement image that corresponds to the atomic structure of a sample surface not only due to interactions between the atom forming the tip of the probe and the measurement subject but also due to interactions between other atoms of the probe and the measurement subject.
Numerical simulation of a measurement image of a scanning probe microscope may be performed to associate a measurement image with the atomic structure of a sample surface. To perform numerical simulation with the measurement image of a scanning probe microscope, two approaches have mainly been used.
One of the approaches is a bottom-up approach, in which the acting force is calculated at the atomic level and measurements are performed at a plurality of discrete probe scanning positions to form a coarse-grained simulation image. More specifically, this approach includes the steps described below:
Step 1: The probe tip atom is moved to a point (X, Y) within an xy plane.
Step 2: The probe tip atom is moved to point Z on the z axis, which is orthogonal to the xy plane. As a result, the probe tip atom will be at coordinates (X, Y, Z).
Step 3: Referring to FIG. 13, an acting force F between all probe atoms and sample atoms is calculated.
Step 4: The processing returns to step 2, in which the probe tip atom is moved to another point Z. Steps 2 and 3 are repeated to obtain a graph indicating the acting force (F(Z)) shown in FIG. 14(a).
Step 5: The height Z0 at which F(Z0) is equal to F0 for an acting force value F0 is determined.
Step 6: As shown in FIG. 14(b), the processing returns to step 1, and steps 1 to 5 are repeated to obtain a two-dimensional distribution (Z0 (x, y)) of the height Z0.
The bottom-up approach described above has been successful when the subject is the surface of an inorganic solid.
The other one of the approaches is a top-down approach, in which a coarse-grained simulation image of a biomolecule and a probe is formed by assuming that the biomolecule and the probe are a continuum, and an interaction between the biomolecule and the probe is analyzed using the finite element method. This approach requires less time for calculations than the bottom-up approach.    Patent Document 1: Japanese Laid-Open Patent Publication No. 62-130302 (p. 1, FIG. 1)    Patent Document 2: Japanese Laid-Open Patent Publication No. 2004-279349 (p. 1, FIGS. 2 and 3)    Patent Document 3: Japanese Laid-Open Patent Publication No. 8-178935 (p. 1, FIGS. 1 to 3)